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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttaactctctgaatcccaacattggaagcacttctctattctttttatcatgtatgcttttgcaaaccatcctggcatcctgctacagacagaactgtattatctgtttattttggaaggcattgttatgctaaatccaaaatgaagtgctaaaagaaatactgacacttgtgcagATAACTTGGCTGCCAACTTCAGCAGGGAACTGGCAGACTACATAATCTACATCATCGATGTTTCTGGTGGGGACAAAATACCAAGAAAAGGTGGCCCTGG

Basic information

species Oryza sativa
transcript LOC_Os05g49050.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g49050.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G413652_T01 (Zea mays), 3'ss of exon 4
gtatttaactctctgaatcccaacattggaagcacttctctattctttttatcatgtatgcttttgcaaaccatcctggcatcctgctacagacagaactgtattatctgtttattttggaaggcattgttatgctaaatccaaaatgaagtgctaaaagaaatactgacacttgtgcagATAACTTGGCTGCCAACTTCAGCAGGGAACTGGCAGACTACATAATCTACATCATCGATGTTTCTGGTGGGGACAAAATACCAAGAAAAGGTGGCCCTGG
                                                                || |||||   | ||  |||||  | |     | |      |||  | |  ||  |||   |||   |     ||||||  || ||    |   |    | |     |   ||||||||||||||| || ||||||||||| ||| | |||||||||||||||||||| |||||||| |||||||||||||| |||||||||||||||||||||||
----------------------------------------------------------------tg-aaacc--tcaggtgtcctga-atatgtcaagc------atccctctggttctgaaaa-atttcaac----aatccagcattaaagagtgccatttgtgccttttcc-atgcagATAACTTGGCAGCTAACTTCAGCAGAGAATTAGCAGACTACATAATCTACATTATCGATGTCTCTGGTGGGGACAAGATACCAAGAAAAGGTGGCCCTGG

upper sequence: LOC_Os05g49050.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA08G08970.1 (Glycine max), 3'ss of exon 3
gtatttaactctctgaatcccaacattggaagcacttctctattctttttatcatgtatgcttttgcaaaccatcctggcatcctgctacagacagaactgtattatctgtttattttggaaggcattgttatgctaaatccaaaatg----aagtgctaaaagaaatactgacacttgtgcagATAACTTGGCTGCCAACTTCAGCAGGGAACTGGCAGACTACATAATCTACATCATCGATGTTTCTGGTGGGGACAAAATACCAAGAAAAGGTGGCCCTGG
                                                                            ||  |||   ||    |  | |||    ||| |  || ||||  ||       ||| | || |||| ||| |       |  | |    | |  |    ||| |||||||||| |||||||||| |||||||||||| |||| ||||| || || ||||| || || || ||||| || || ||||| ||  | |||||||| |||||
--------------------------------------------------------------------------tatgatatcaatct---tattgcacttacatatgtcattgttttttaaa------ttaagttagatcccaaaagctttggatattcacttgagt-ttctttcttctgcagATAACCTGGCTGCCAATTTCAGCAGGGAATTGGCTGACTATATTATTTACATAATAGACGTGTCTGGCGGTGATAAAATTCCTCGGAAAGGTGGTCCTGG

upper sequence: LOC_Os05g49050.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT2G34470.2 (Arabidopsis thaliana), 3'ss of exon 4
gtatttaactctctgaatcccaacattggaagcacttctctattctttttatcatgtatgcttttgcaaaccatcctggcatcctgctacagacagaactgtattatctgtttattttggaaggcattgttatgctaaatccaaaatgaagtgctaaaagaaatactgacacttgt-gcagATAACTTGGCTGCCAACTTCAGCAGGGAACTGGCAGACTACATAATCTACATCATCGATGTTTCTGGTGGGGACAAAATACCAAGAAAAGGTGGCCCTGG
                                                       ||  | |||         | || ||    |  |        | ||| |  || | |  ||||  |      || | | |   || |   |||||  |   || ||   || ||     ||| |||||||| || ||||| || ||||| || ||||| || ||||| || ||||||||||||||||| || | ||| || ||||||||  | ||||| ||||||||
-------------------------------------------------------gtgaggtttcat------ttctagctagttcttgatagttaatctgcacgatatatagatttctgt-----ttctcaag--gaacc---aatgagatatgaataggcttagtgttgtgtgttgcagATAATTTAGCTGCTAATTTCAGTAGAGAACTAGCTGACTATATCATCTACATCATCGATGTATCGGCTGGTGATAAAATACCCCGTAAAGGCGGCCCTGG

upper sequence: LOC_Os05g49050.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv10s0003g03120.t01 (Vitis vinifera), 3'ss of exon 8
gtatttaactctctgaatcccaacattggaagcacttctctattctttttatcatgtatgcttttgcaaaccatcctggcatcctgctacagacagaactgtattatctgtttattttggaaggcattgttatgctaaatccaaaatgaagtgctaaaagaaatactgacacttgtg------cagATAACTTGGCTGCCAACTTCAGCAGGGAACTGGCAGACTACATAATCTACATCATCGATGTTTCTGGTGGGGACAAAATACCAAGAAAAGGTGGCCCTGG
                                                                            |  || | | | |  |||         |  | | |  ||  |  |||| ||  || || ||| |     || |   | |  || |  ||||   | |||||      ||||||| || |||||||| |||||||||||| |||| ||||| || || || || || ||||| |||||||| |||||||| ||  | ||||| ||||| ||
----------------------------------------------------------------------------taacaacttaccattgac---------tcgtttatggatacttaaaggaatgtttttgataa-tttgggataagaaggtttaacatttacttcaatttgtgtcactgcagATAATTTAGCTGCCAATTTCAGCAGGGAATTGGCCGACTATATTATTTATATAATAGATGTATCTGGTGGTGACAAAATTCCTCGGAAAGGAGGCCCAGG

upper sequence: LOC_Os05g49050.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S101_185V6.4 (Physcomitrella patens), 3'ss of exon 5
gtatttaactctctgaatcccaacattggaagcacttctctattctttttatcatgtat-gcttttgcaaaccatcctggcatcctgctacagacagaactgtattatctgtttattttggaaggcattgttatgctaaatccaaaatgaagtgctaaaagaaatactgacacttgtgcagATAACTTGGCTGCCAACTTCAGCAGGGAACTGGCAGACTACATAATCTACATCATCGATGTTTCTGGTGGGGACAAAATACCAAGAAAAGGTGGCCCTGG
||| | |   ||| | |||  |  |  || |    |  |          |  || ||||  | | ||   |  ||  |    |   | | ||  |  || || |||     |  | ||| |||     | |  ||   || ||       | | ||  |     |  |||   || |||||| ||  | || || |||||||||||||| |||||||||||||| || |||||||| ||||| || ||||| || ||||| ||  | || ||||| || ||
gtaat-actcctcagtatcttattac-ggtattgttaattggactggaattacacgtattacctgtgtttaa-atgataatgtaaagtttcattcgaaattggatt-----tggagtttcgaa-----tttcttgaagaagcctgttgttaatcctcgagtttgttgtgagttttctgcagACAATCTAGCGGCAAACTTCAGCAGGGAGCTGGCAGACTACATTATTTACATCATTGATGTATCCGGTGGTGATAAAATTCCTCGCAAGGGTGGTCCAGG

upper sequence: LOC_Os05g49050.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ21803 (Selaginella moellendorffii), 3'ss of exon 4
gtatttaactctctgaatcccaacattggaagcacttctctattctttttatcatgtatgcttttgcaaaccatcctggcatcctgctacagacagaactgtattatctgtttattttggaaggcattgttatgctaaatccaaaatgaagtgctaaaagaaata--ctgacacttgt--gcagATAACTTGGCTGCCAACTTCAGCAGGGAACTGGCAGACTACATAATCTACATCATCGATGTTTCTGGTGGGGACAAAATACCAAGAAAAGGTGGCCCTGG
                                                                                                                                           |  || |     | |||    || ||    |   |||||  ||||||||| | || || ||||||||||||||||| || |||||||| ||||| || |||||||| ||||| || |||||||| ||  | ||||| || |||||
------------------------------------------------------------------------------------------------------------------------------------------gtataacactgttttctaccgcaactaactcgtttcttgtttgcagATAACCTCGCGGCAAACTTCAGCAGGGAACTAGCCGACTACATCATCTATATTATCGATGTCTCTGGGGGCGACAAAATTCCTCGCAAAGGCGGGCCTGG

upper sequence: LOC_Os05g49050.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ34189 (Selaginella moellendorffii), 3'ss of exon 4
gtatttaactctctgaatcccaacattggaagcacttctctattctttttatcatgtatgcttttgcaaaccatcctggcatcctgctacagacagaactgtattatctgtttattttggaaggcattgttatgctaaatccaaaatgaagtgctaaaagaaata--ctgacacttgt--gcagATAACTTGGCTGCCAACTTCAGCAGGGAACTGGCAGACTACATAATCTACATCATCGATGTTTCTGGTGGGGACAAAATACCAAGAAAAGGTGGCCCTGG
                                                                                                                                           | ||| |     | |||    || ||    |   |||||  ||||||||| | || || ||||||||||||||||| || |||||||| ||||| || |||||||| ||||| || |||||||| ||  | ||||| || |||||
------------------------------------------------------------------------------------------------------------------------------------------gtacaacactgttttctaccgcaactaactcgtttcttgtttgcagATAACCTCGCCGCAAACTTCAGCAGGGAACTAGCCGACTACATCATCTATATTATCGATGTCTCTGGGGGCGACAAAATTCCTCGCAAAGGCGGGCCTGG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|313080743|gb|HO213540.1|HO213540
EST:     ACTATCAAACTTGTACAAAGCTGATTTACTCCTCTGTGAATCTGGAGGAG                         ATAACTTGGCTGCCAACTTCAGCAGGGAACTGGCAGACTACATAATCTACA
genomic: ACTATCAAACTTGTGCAAAGCTGATTTACTCCTCTGTGAATCTGGAGGAGgtatttaact ... acttgtgcagATAACTTGGCTGCCAACTTCAGCAGGGAACTGGCAGACTACATAATCTACA
EST: gi|88841450|gb|CI005530.1|CI005530
EST:     TATCAAACTTGTGCAAAGCTGATTTACTCCTCTGTGAATCTGGAGGAG                         ATAACTTGGCTGCCAACTTCAGCAGGGAACTGGCAGACTACATAATCTACA
genomic: TATCAAACTTGTGCAAAGCTGATTTACTCCTCTGTGAATCTGGAGGAGgtatttaact ... acttgtgcagATAACTTGGCTGCCAACTTCAGCAGGGAACTGGCAGACTACATAATCTACA
EST: gi|58589567|gb|CF987875.1|CF987875
EST:     ACTATCAAACTTGTACAAAGCTGATTGACTCCTCTGTGAATCTGGAGGAG                         ATAACTTGGCTGCCAACTTCAGCAGGGAACTGGCAGACTACATAATCTACA
genomic: ACTATCAAACTTGTGCAAAGCTGATTTACTCCTCTGTGAATCTGGAGGAGgtatttaact ... acttgtgcagATAACTTGGCTGCCAACTTCAGCAGGGAACTGGCAGACTACATAATCTACA
EST: gi|88218494|gb|CI218343.1|CI218343
EST:     ACTATCAAACTTGTGCAAAGCTGATTTACTCCTCTGTGAATCTGGAGGAG                         ATAACTTGGCTGCCAACTTCAGCAGGGAACTGGCAGACTACATAATCTACA
genomic: ACTATCAAACTTGTGCAAAGCTGATTTACTCCTCTGTGAATCTGGAGGAGgtatttaact ... acttgtgcagATAACTTGGCTGCCAACTTCAGCAGGGAACTGGCAGACTACATAATCTACA
EST: gi|89170224|gb|CI039501.1|CI039501
EST:     ACTATCAAACTTGTGCAAAGCTGATTTACTCCTCTGTGAATCTGGAGGAG                         ATAACTTGGCTGCCAACTTCAGCAGGGAACTGGCAGACTACATAATCTACA
genomic: ACTATCAAACTTGTGCAAAGCTGATTTACTCCTCTGTGAATCTGGAGGAGgtatttaact ... acttgtgcagATAACTTGGCTGCCAACTTCAGCAGGGAACTGGCAGACTACATAATCTACA
EST: gi|58668597|gb|CK057283.1|CK057283
EST:     ACTATCAAACTTGTACAAAGCTGATTTACTCCTCTGTGAATCTGGAGGAG                         ATAACTTGGCTGCCAACTTCAGCAGGGAACTGGCAGACTACATAATCTACA
genomic: ACTATCAAACTTGTGCAAAGCTGATTTACTCCTCTGTGAATCTGGAGGAGgtatttaact ... acttgtgcagATAACTTGGCTGCCAACTTCAGCAGGGAACTGGCAGACTACATAATCTACA
EST: gi|86532427|gb|CI172633.1|CI172633
EST:     GTGAATCTGGAGGAG                         ATAACTTGGCTGCCAACTTCAGCAGGGAACTGGCAGACTACATAATCTACA
genomic: GTGAATCTGGAGGAGgtatttaact ... acttgtgcagATAACTTGGCTGCCAACTTCAGCAGGGAACTGGCAGACTACATAATCTACA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 58 (upstream exon), 67 (downstream exon)
Score: 20

CACGCTGCAATACGTGAGGACATCAGCATAAATCTAGGTCCTCTGGAAGAACTATCAAACTTGTGCAAAGCTGATTTACTCCTCTGTGAATCTGGAGGAGgtatttaact ... acttgtgcagATAACTTGGCTGCCAACTTCAGCAGGGAACTGGCAGACTACATAATCTACATCATCGATGTTTCTGGTGGGGACAAAATACCAAGAAAAGGTGGCCCTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgttatgctaaatccaaaatgaagtgctaaaagaaatactgacacttgtgcagATAACTTGGCTGCCAACTTCAGCAGGGAACTGGCAGACTACATAATCTACATCATCGATGTTTCTGGTGGGGACAAAATACCAAGAAAAGGTGGCCCTGG
                                      tactgac  putative branch site (score: 20)
                             taaaagaaata  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttaactctctgaatcccaacattggaagcacttctctattctttttatcatgtatgcttttgcaaaccatcctggcatcctgctacagacagaactgtattatctgtttattttggaaggcattgttatgctaaatccaaaatgaagtgctaaaagaaatactgacacttgtgcagATAACTTGGCTGCCAACTTCAGCAGGGAACTGGCAGACTACATAATCTACATCATCGATGTTTCTGGTGGGGACAAAATACCAAGAAAAGGTGGCCCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA